Telling plant species apart with DNA: From barcodes to genomes

Land plants underpin a multitude of ecosystem functions, support human livelihoods and represent a critically important component of terrestrial biodiversity - yet many tens of thousands of species await discovery, and plant identification remains a substantial challenge, especially where material is juvenile, fragmented, or processed. In this Opinion article we tackle two main topics. Firstly we provide a short summary of the strengths and limitations of plant DNA barcoding for addressing these issues. We secondly discuss options for enhancing current plant barcodes, focusing on increasing discriminatory power via either gene capture of nuclear markers or genome skimming. The former has the advantage of establishing a defined set of target loci maximising efficiency of sequencing effort, data storage and analysis. The challenge is developing a probe set for large numbers of nuclear markers that works over sufficient phylogenetic breadth. Genome skimming has the advantage of using existing protocols, being backward compatible with existing barcodes, and the depth of sequence coverage can be increased as sequencing costs fall. Its non-targeted nature, does however present a major informatics challenge for upscaling to large sample sets.